curious.bio/planktoscope
curious.bio/planktoscope
8
0
Fork 0
Code Issues 10 Pull requests Packages Projects 7 Releases Wiki Activity

flow: add mL to concentrated sample volume and add process_description field to metadata

Browse source
This commit is contained in:
Romain Bazile 2020-12-03 15:15:13 +01:00
parent 981dd12646
commit 68d2a10303
1 changed files with 90 additions and 88 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

178
flows/main.json
View file

@ -741,24 +741,6 @@
"width": 5,
"height": 1
},
{
"id": "226903fb.014ba4",
"type": "ui_spacer",
"name": "spacer",
"group": "3e1ba03d.f01d8",
"order": 9,
"width": 5,
"height": 1
},
{
"id": "a393ee49.38373",
"type": "ui_spacer",
"name": "spacer",
"group": "cf5d9f0e.d57e7",
"order": 13,
"width": 4,
"height": 1
},
{
"id": "a7d64879.38298",
"type": "ui_group",
@ -875,6 +857,24 @@
"width": 8,
"height": 1
},
{
"id": "692eec9a.2996cc",
"type": "ui_spacer",
"name": "spacer",
"group": "3e1ba03d.f01d8",
"order": 10,
"width": 5,
"height": 1
},
{
"id": "9c34106a.4c5998",
"type": "ui_spacer",
"name": "spacer",
"group": "cf5d9f0e.d57e7",
"order": 13,
"width": 4,
"height": 1
},
{
"id": "4e78af2d.90be7",
"type": "ui_ui_control",
@ -1837,7 +1837,7 @@
"delay": "1000",
"topic": "sample_ship",
"x": 670,
"y": 340,
"y": 80,
"wires": [
[
"9f501f49.45645"
@ -1893,7 +1893,7 @@
"payload": "",
"topic": "sample_sampling_gear",
"x": 630,
"y": 460,
"y": 200,
"wires": [
[
"9f501f49.45645",
@ -1917,7 +1917,7 @@
"delay": "1000",
"topic": "sample_operator",
"x": 650,
"y": 420,
"y": 160,
"wires": [
[
"9f501f49.45645",
@ -1941,7 +1941,7 @@
"delay": "1000",
"topic": "sample_project",
"x": 660,
"y": 300,
"y": 40,
"wires": [
[
"9f501f49.45645"
@ -1964,7 +1964,7 @@
"delay": "1000",
"topic": "sample_id",
"x": 670,
"y": 380,
"y": 120,
"wires": [
[
"9f501f49.45645"
@ -1982,7 +1982,7 @@
"initialize": "",
"finalize": "",
"x": 1080,
"y": 460,
"y": 200,
"wires": [
[]
]
@ -2061,8 +2061,8 @@
"z": "b771c342.49603",
"name": "",
"events": "change",
"x": 460,
"y": 1300,
"x": 340,
"y": 880,
"wires": [
[]
]
@ -2081,8 +2081,8 @@
"raw": false,
"topic": "",
"name": "",
"x": 770,
"y": 1420,
"x": 650,
"y": 1000,
"wires": [
[]
]
@ -2097,8 +2097,8 @@
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 470,
"y": 1360,
"x": 350,
"y": 940,
"wires": [
[
"726a7822.cd6298",
@ -2126,8 +2126,8 @@
"device": false,
"gst": false,
"att": false,
"x": 290,
"y": 1420,
"x": 170,
"y": 1000,
"wires": [
[]
]
@ -2138,8 +2138,8 @@
"z": "b771c342.49603",
"name": "",
"events": "change",
"x": 760,
"y": 1340,
"x": 640,
"y": 920,
"wires": [
[]
]
@ -2160,7 +2160,7 @@
"delay": "1000",
"topic": "object_lat",
"x": 620,
"y": 820,
"y": 560,
"wires": [
[
"7953b1b2.d53ed8"
@ -2183,7 +2183,7 @@
"delay": "1000",
"topic": "object_lon",
"x": 610,
"y": 860,
"y": 600,
"wires": [
[
"7953b1b2.d53ed8"
@ -2203,7 +2203,7 @@
"passthru": true,
"topic": "object_date",
"x": 1250,
"y": 820,
"y": 560,
"wires": [
[
"29f2b365.4327ec"
@ -2226,7 +2226,7 @@
"delay": 300,
"topic": "object_time",
"x": 1250,
"y": 860,
"y": 600,
"wires": [
[
"1a945afa.d60aad"
@ -2591,8 +2591,8 @@
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 300,
"y": 1300,
"x": 180,
"y": 880,
"wires": [
[
"222c851d.5d0a3a"
@ -2617,8 +2617,8 @@
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 300,
"y": 1360,
"x": 180,
"y": 940,
"wires": [
[
"986d960a.c75908"
@ -3522,7 +3522,7 @@
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "Encapsulate config",
"func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera_name\": global.get(\"acq_camera_name\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object_lat\"),\n\t\t\"object_lon\": global.get(\"object_lon\"),\n\t\t\"object_depth_min\": global.get(\"object_depth_min\"),\n\t\t\"object_depth_max\": global.get(\"object_depth_max\"),\n\n\t\t\"process_pixel\": global.get(\"process_pixel\"),\n\t\t\"process_id\": global.get(\"process_id\")\n\t}\n};\n\nif (msg.payload.config.sample_sampling_gear == \"net\") {\n\tmsg.payload.config = { ...msg.payload.config ,\n\t\t\t\"sample_gear_net_opening\": global.get(\"sample_gear_net_opening\"),\n\t\t\t\"object_date_end\": global.get(\"object_date_end\"),\n\t\t\t\"object_time_end\": global.get(\"object_time_end\"),\n\t\t\t\"object_lat_end\": global.get(\"object_lat_end\"),\n\t\t\t\"object_lon_end\": global.get(\"object_lon_end\")\n\t};\n}\nreturn msg;",
"func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n \t\"description\": {\n \t\t\"sample_project\": \"Project's name\",\n \t\t\"sample_id\": \"Sample ID\",\n \t\t\"sample_uuid\": \"Sample UUID (Autogenerated)\",\n \t\t\"sample_ship\": \"Ship's name\",\n \t\t\"sample_operator\": \"Operator's name\",\n \t\t\"sample_sampling_gear\": \"Sampling gear used\",\n \t\t\"sample_concentrated_sample_volume\": \"Volume of concentrated sample, in mL\",\n \t\t\"acq_id\": \"Acquisition ID\",\n \t\t\"acq_uuid\": \"Acquisition UUID (Autogenerated)\",\n \t\t\"acq_instrument\": \"Instrument type\",\n \t\t\"acq_instrument_id\": \"Instrument ID\",\n \t\t\"acq_celltype\": \"Flow cell dimension thickness, in µm\",\n \t\t\"acq_minimum_mesh\": \"Minimum filtration mesh size, in µm\",\n \t\t\"acq_maximum_mesh\": \"Maximum filtration mesh size, in µm\",\n \t\t\"acq_min_esd\": \"\",\n \t\t\"acq_max_esd\": \"\",\n \t\t\"acq_volume\": \"Imaged volume, in mL\",\n \t\t\"acq_magnification\": \"Optical magnification\",\n \t\t\"acq_fnumber_objective\": \"Focal length of the objective, in mm\",\n \t\t\"acq_camera_name\": \"Name of the camera used\",\n \t\t\"acq_nb_frame\": \"Number of picture taken\",\n \"acq_local_datetime\": \"Instrument local datetime\",\n \"acq_camera_resolution\": \"Resolution of the images\",\n \"acq_camera_iso\": \"ISO Number of the images\",\n \"acq_camera_shutter_speed\": \"Shutter speed of the images, in µs\",\n \t\t\"object_date\": \"Sample collection date (or beginning if using a net)\",\n \t\t\"object_time\": \"Sample collection time (or beginning if using a net)\",\n \t\t\"object_lat\": \"Sample collection latitude (or beginning if using a net)\",\n \t\t\"object_lon\": \"Sample collection longitude (or beginning if using a net)\",\n \t\t\"object_depth_min\": \"Sample collection minimal depth, in m\",\n \t\t\"object_depth_max\": \"Sample collection maximum depth, in m\",\n \t\t\"process_pixel\": \"Pixel imaging resolution, in µm/pixel\",\n \t\t\"process_id\": \"Segmentation ID\",\n \t\t\"process_uuid\": \"Segmentation UUID (Autogenerated)\",\n \t\t\"sample_gear_net_opening\": \"Sample mouth opening dimension, in mm\",\n \t\t\"object_date_end\": \"Sample end collection date when using a net\",\n \t\t\"object_time_end\": \"Sample end collection time when using a net\",\n \t\t\"object_lat_end\": \"Sample end collection latitude when using a net\",\n \t\t\"object_lon_end\": \"Sample end collection longitude when using a net\",\n \t},\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera_name\": global.get(\"acq_camera_name\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object_lat\"),\n\t\t\"object_lon\": global.get(\"object_lon\"),\n\t\t\"object_depth_min\": global.get(\"object_depth_min\"),\n\t\t\"object_depth_max\": global.get(\"object_depth_max\"),\n\n\t\t\"process_pixel\": global.get(\"process_pixel\"),\n\t\t\"process_id\": global.get(\"process_id\")\n\t}\n};\n\nif (msg.payload.config.sample_sampling_gear == \"net\") {\n\tmsg.payload.config = { ...msg.payload.config ,\n\t\t\t\"sample_gear_net_opening\": global.get(\"sample_gear_net_opening\"),\n\t\t\t\"object_date_end\": global.get(\"object_date_end\"),\n\t\t\t\"object_time_end\": global.get(\"object_time_end\"),\n\t\t\t\"object_lat_end\": global.get(\"object_lat_end\"),\n\t\t\t\"object_lon_end\": global.get(\"object_lon_end\")\n\t};\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
@ -3629,7 +3629,7 @@
"initialize": "",
"finalize": "",
"x": 330,
"y": 300,
"y": 40,
"wires": [
[
"9c882b37.fde668"
@ -3647,7 +3647,7 @@
"initialize": "",
"finalize": "",
"x": 330,
"y": 340,
"y": 80,
"wires": [
[
"4557d689.a4fa88"
@ -3665,7 +3665,7 @@
"initialize": "",
"finalize": "",
"x": 320,
"y": 380,
"y": 120,
"wires": [
[
"94eb4221.9b92c"
@ -3683,7 +3683,7 @@
"initialize": "",
"finalize": "",
"x": 340,
"y": 420,
"y": 160,
"wires": [
[
"82c5fc77.59c97"
@ -3695,11 +3695,13 @@
"type": "function",
"z": "b771c342.49603",
"name": "get sample_sampling_gear",
"func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;",
"func": "if (msg.payload.sample_sampling_gear === null){\n msg.payload = \"net\";\n}\nelse\n{\n msg.payload = msg.payload.sample_sampling_gear;\n}\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 460,
"y": 200,
"wires": [
[
"fcfc31ae.af3af"
@ -3834,7 +3836,7 @@
"name": "",
"env": [],
"x": 90,
"y": 380,
"y": 120,
"wires": [
[
"d027a6bf.7049e8",
@ -3851,8 +3853,8 @@
"z": "b771c342.49603",
"name": "",
"env": [],
"x": 750,
"y": 1380,
"x": 630,
"y": 960,
"wires": [
[]
]
@ -3873,7 +3875,7 @@
"delay": "1000",
"topic": "object_lat_end",
"x": 600,
"y": 940,
"y": 680,
"wires": [
[
"7953b1b2.d53ed8"
@ -3896,7 +3898,7 @@
"delay": "1000",
"topic": "object_lon_end",
"x": 600,
"y": 980,
"y": 720,
"wires": [
[
"7953b1b2.d53ed8"
@ -3916,7 +3918,7 @@
"passthru": true,
"topic": "object_date_end",
"x": 1230,
"y": 940,
"y": 680,
"wires": [
[
"29f2b365.4327ec"
@ -3939,7 +3941,7 @@
"delay": 300,
"topic": "object_time_end",
"x": 1230,
"y": 980,
"y": 720,
"wires": [
[
"1a945afa.d60aad"
@ -3957,7 +3959,7 @@
"initialize": "",
"finalize": "",
"x": 1540,
"y": 860,
"y": 600,
"wires": [
[]
]
@ -3973,7 +3975,7 @@
"initialize": "",
"finalize": "",
"x": 1540,
"y": 820,
"y": 560,
"wires": [
[]
]
@ -4202,8 +4204,8 @@
"d": true,
"name": "GPS Status",
"scope": [],
"x": 310,
"y": 1500,
"x": 190,
"y": 1080,
"wires": [
[
"7116e906.9f50f"
@ -4223,8 +4225,8 @@
"label": "GPS Status:",
"format": "{{msg.status.text}}",
"layout": "row-left",
"x": 810,
"y": 1500,
"x": 690,
"y": 1080,
"wires": []
},
{
@ -4356,7 +4358,7 @@
"label": "Object depth Max",
"tooltip": "",
"group": "3e1ba03d.f01d8",
"order": 7,
"order": 8,
"width": 5,
"height": 1,
"passthru": true,
@ -4364,7 +4366,7 @@
"delay": "1000",
"topic": "object_depth_max",
"x": 650,
"y": 540,
"y": 280,
"wires": [
[
"9f501f49.45645"
@ -4379,7 +4381,7 @@
"label": "Object Depth Min",
"tooltip": "",
"group": "3e1ba03d.f01d8",
"order": 6,
"order": 7,
"width": 5,
"height": 1,
"passthru": true,
@ -4387,7 +4389,7 @@
"delay": "1000",
"topic": "object_depth_min",
"x": 650,
"y": 580,
"y": 320,
"wires": [
[
"9f501f49.45645"
@ -5108,7 +5110,7 @@
"35eb925e.5f8016"
],
"x": 815,
"y": 420,
"y": 160,
"wires": []
},
{
@ -5507,7 +5509,7 @@
"repair": false,
"outputs": 2,
"x": 1090,
"y": 420,
"y": 160,
"wires": [
[
"66b362ee.80b5b4"
@ -5544,7 +5546,7 @@
"to": "",
"reg": false,
"x": 1290,
"y": 400,
"y": 140,
"wires": [
[
"cbb123ab.fd3428"
@ -5578,7 +5580,7 @@
"to": "",
"reg": false,
"x": 1300,
"y": 440,
"y": 180,
"wires": [
[
"cbb123ab.fd3428"
@ -5592,7 +5594,7 @@
"name": "",
"events": "change",
"x": 1500,
"y": 420,
"y": 160,
"wires": [
[]
]
@ -5613,7 +5615,7 @@
"delay": "1000",
"topic": "object_lat",
"x": 620,
"y": 700,
"y": 440,
"wires": [
[
"7953b1b2.d53ed8"
@ -5636,7 +5638,7 @@
"delay": "1000",
"topic": "object_lon",
"x": 610,
"y": 740,
"y": 480,
"wires": [
[
"7953b1b2.d53ed8"
@ -5656,7 +5658,7 @@
"passthru": true,
"topic": "object_date",
"x": 1250,
"y": 700,
"y": 440,
"wires": [
[
"29f2b365.4327ec"
@ -5679,7 +5681,7 @@
"delay": 300,
"topic": "object_time",
"x": 1250,
"y": 740,
"y": 480,
"wires": [
[
"1a945afa.d60aad"
@ -5701,7 +5703,7 @@
"resendOnRefresh": true,
"templateScope": "local",
"x": 590,
"y": 780,
"y": 520,
"wires": [
[]
]
@ -5721,7 +5723,7 @@
"resendOnRefresh": true,
"templateScope": "local",
"x": 590,
"y": 900,
"y": 640,
"wires": [
[]
]
@ -5903,10 +5905,10 @@
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "sample_concentrated_sample_volume",
"label": "Concentrated sample volume",
"tooltip": "Volume extracted from the net",
"label": "Concentrated sample volume (mL)",
"tooltip": "Volume extracted from the net (in mL)",
"group": "3e1ba03d.f01d8",
"order": 8,
"order": 9,
"width": 5,
"height": 1,
"passthru": true,
@ -5914,7 +5916,7 @@
"delay": "1000",
"topic": "sample_concentrated_sample_volume",
"x": 590,
"y": 500,
"y": 240,
"wires": [
[
"9f501f49.45645"
@ -5937,7 +5939,7 @@
"delay": "1000",
"topic": "sample_gear_net_opening",
"x": 620,
"y": 620,
"y": 360,
"wires": [
[
"9f501f49.45645"
@ -6117,7 +6119,7 @@
"tooltip": "",
"place": "Coordinates type",
"group": "3e1ba03d.f01d8",
"order": 5,
"order": 6,
"width": 0,
"height": 0,
"passthru": true,
@ -6137,7 +6139,7 @@
"payload": "",
"topic": "coordinates_type",
"x": 590,
"y": 1020,
"y": 760,
"wires": [
[
"8318ab20.aa34f8"
@ -6155,7 +6157,7 @@
"initialize": "",
"finalize": "",
"x": 870,
"y": 840,
"y": 580,
"wires": [
[
"9f501f49.45645"
@ -6187,7 +6189,7 @@
"topic": "",
"name": "",
"x": 1070,
"y": 860,
"y": 600,
"wires": [
[]
]
@ -6203,7 +6205,7 @@
"initialize": "",
"finalize": "",
"x": 780,
"y": 1020,
"y": 760,
"wires": [
[]
]
@ -6230,7 +6232,7 @@
"payload": "dd",
"payloadType": "str",
"x": 390,
"y": 1020,
"y": 760,
"wires": [
[
"db44a49e.960558"